AtomLens Help
Obscure Essentials
Updated: February 21, 2026
Quick summary
- Open molecule files and AtomLens renders a clean 2D structure view automatically.
- Generate identifiers (SMILES/InChI/InChI Key) and core molecular properties in one place.
- Search chemistry files locally with Spotlight metadata and Quick Look previews.
- Standard use is local-first: your structures stay on your Mac.
Contents
Quick Start
If you are new to AtomLens, start here.
- Open a file using File > Open… or the toolbar Open button.
- For opened files, AtomLens detects format and renders immediately.
- For text you type or paste, click Parse & Render.
- Parse & Render is enabled only when a valid structure format is detected.
- Use canvas controls to zoom, rotate, pan, and reset view.
Main Workflow
A typical session has five steps:
- Load and inspect: read molecular files and inspect 2D structure depictions.
- Compute identifiers: SMILES, ISO SMILES, InChI, and InChI Key.
- Compute properties: formula, molecular weight, monoisotopic mass, LogP, and Rule-of-Five related values.
- Search locally: query Spotlight-indexed chemistry files from inside AtomLens.
- Export and share: export to common chemistry formats or SVG.
Interface Overview
The interface is organized into practical zones.
- Input sidebar (left): editable source text plus detected format indicator.
- Canvas (center): Metal-rendered 2D depiction with pan/zoom/rotation.
- Overview sidebar (right): identifiers and calculated properties.
- Toolbar controls: Open, Search, Help, sidebar toggles, and depiction-style switches.
- Canvas utilities: zoom slider, rotation slider (0-360), reset, snapshot to clipboard (transparent PNG).
- Layout persistence: window frame and sidebar widths are restored across launches.
Supported Input Formats
AtomLens can open these file types directly.
| Format | Extensions | UTI |
|---|---|---|
| MDL Molfile | .mol | de.losko.atomlens.molfile |
| MDL SDFile | .sdf, .sd | de.losko.atomlens.sdfile |
| SMILES | .smi, .smiles, .ism, .can | de.losko.atomlens.smiles |
| InChI | .inchi, .ich | de.losko.atomlens.inchi |
| Tripos MOL2 | .mol2 | de.losko.atomlens.mol2 |
| Protein Data Bank | .pdb, .ent | de.losko.atomlens.pdb |
| XYZ Coordinates | .xyz | de.losko.atomlens.xyz |
| Chemical Markup Language | .cml | de.losko.atomlens.cml |
| MDL RXN | .rxn | de.losko.atomlens.rxn |
| MDL RDF | .rdf | de.losko.atomlens.rdf |
| Plain text (auto-detect) | .txt | public.plain-text |
Supported Export Formats
Use File > Export… and choose a format in the save dialog.
| Export format | Extensions | Notes |
|---|---|---|
| SVG depiction | .svg | Uses current visualization style settings. |
| MDL Molfile (V2000) | .mol | Single structure. |
| MDL SDFile | .sdf, .sd | Single or multiple structures. |
| SMILES | .smi, .smiles, .can | Standard flavor. |
| SMILES (Isomeric) | .ism | Stereochemistry-aware output. |
| InChI | .inchi, .ich | Native Swift CDK-derived generation path. |
| Tripos MOL2 | .mol2 | Text export. |
| Protein Data Bank | .pdb, .ent | Text export. |
| XYZ Coordinates | .xyz | Text export. |
| Chemical Markup Language | .cml | XML export. |
| MDL RXN | .rxn | Reaction output from current set. |
| MDL RDF | .rdf | Reaction-data output from current set. |
Extract: Split Multi-Structure SDF
Use this when one SDF file contains many compounds and you want separate files.
- Choose
File > Extract > Split multi-structure SDF into multiple files…. - Select an SDF file with more than one structure.
- AtomLens reports structure count and asks for a target folder.
- Each structure is saved as an individual
.sdffile (molecule name is used when available). - A progress dialog shows real-time save progress and failed entries.
Molecule Search Panel
The search panel helps you browse large local structure collections quickly.
- Open via the toolbar Search button.
- Uses Spotlight index metadata for fast local search.
- Incremental results: entries appear while Spotlight continues searching.
- Lazy preview loading prioritizes visible cards for smooth browsing.
- Sort keys: Modified Date, Created Date, Molecular Weight, and LogP.
- Sort order: Ascending or Descending.
- Single-click selects, double-click opens in AtomLens.
Spaceopens Quick Look preview; pressSpaceagain to close.- Panel size is remembered between launches.
Why Spotlight and Quick Look Matter
In real workflows, filenames are often not enough to find the correct structure quickly. AtomLens adds chemistry-aware metadata and visual previews so you can find compounds by properties, not just by filename.
| Feature | Practical value |
|---|---|
| Spotlight chemistry attributes | Find files by InChI Key, formula, molecular weight, LogP, and related descriptors. |
| Finder thumbnails | Triaging large folders becomes visual and faster. |
| Interactive Quick Look previews | Inspect structures with pan/zoom directly from Finder and AtomLens search workflows. |
Spotlight Metadata Attributes
AtomLens writes dedicated metadata keys prefixed with de_losko_atomlens_.
| Attribute | Type | Meaning |
|---|---|---|
de_losko_atomlens_is_molecule | Number (0/1) | Structure validity flag for robust molecule filtering. |
de_losko_atomlens_smiles | String | Generated SMILES. |
de_losko_atomlens_iso_smiles | String | Generated isomeric SMILES. |
de_losko_atomlens_inchi | String | Generated InChI. |
de_losko_atomlens_inchi_key | String | Generated InChI Key. |
de_losko_atomlens_formula | String | Molecular formula. |
de_losko_atomlens_molecular_weight | Number | Molecular weight (Da). |
de_losko_atomlens_xlogp | Number | XLogP estimate. |
de_losko_atomlens_molar_mass | Number | Molar mass (g/mol). |
de_losko_atomlens_monoisotopic_mass | Number | Monoisotopic mass (Da). |
de_losko_atomlens_heavy_atom_count | Number | Heavy atom count. |
de_losko_atomlens_hbond_donor_count | Number | H-bond donor count. |
de_losko_atomlens_hbond_acceptor_count | Number | H-bond acceptor count. |
de_losko_atomlens_rotatable_bond_count | Number | Rotatable bond count. |
de_losko_atomlens_ring_count | Number | Ring count. |
de_losko_atomlens_rule_of_five_status | String | Human-readable Rule-of-Five summary. |
de_losko_atomlens_rule_of_five_violations | Number | Rule-of-Five violation count. |
de_losko_atomlens_rule_of_five_evaluated_criteria_count | Number | Number of Rule-of-Five criteria evaluated. |
de_losko_atomlens_rule_of_five_compliant | Number (0/1) | Rule-of-Five compliance flag. |
Spotlight Search Examples
Examples for Terminal-based local search:
Find by exact InChI Key
mdfind 'de_losko_atomlens_inchi_key == "HVQAJTFOCKOKIN-UHFFFAOYSA-N"'Find all molecule files indexed by AtomLens
mdfind 'de_losko_atomlens_is_molecule == 1'Find by molecular-weight range
mdfind 'de_losko_atomlens_molecular_weight >= 200 && de_losko_atomlens_molecular_weight <= 300'Find by LogP threshold
mdfind 'de_losko_atomlens_xlogp > 3.0'Find Rule-of-Five compliant compounds
mdfind 'de_losko_atomlens_rule_of_five_compliant == 1'Chemistry Notes
- Depictions are optimized for communication and review workflows (2D schematic representation).
- AtomLens follows CDK-derived depiction conventions for rings, aromaticity, and stereobond presentation.
- 2D drawings are not a substitute for full 3D conformational analysis.
Third-Party Software and References
| Component | Role in AtomLens | License |
|---|---|---|
| CDKSwiftNativePort (Swift-native CDK-derived implementation) | Parsing, depiction logic, identifier generation, and molecular property calculations. | LGPL-2.1-or-later |
Swift package used by AtomLens: CDKSwiftNativePort on GitHub
AtomLens is based on ideas and methods from the original Chemistry Development Kit (CDK). For scientific work, please cite CDK references where appropriate:
- Willighagen et al. (2017), The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching. doi:10.1186/s13321-017-0220-4
- May and Steinbeck (2014), Efficient ring perception for the Chemistry Development Kit. doi:10.1186/1758-2946-6-3
- Steinbeck et al. (2006), Recent Developments of the Chemistry Development Kit (CDK) - An Open-Source Java Library for Chemo- and Bioinformatics. doi:10.2174/138161206777585274
- Steinbeck et al. (2003), The Chemistry Development Kit (CDK): An Open-Source Java Library for Chemo- and Bioinformatics. doi:10.1021/ci025584y
Privacy Notice
- AtomLens processes your molecule content locally on your Mac.
- AtomLens does not upload structures to cloud services in normal workflows.
- Spotlight and Quick Look keep local macOS indexes and caches for search and preview.
- Recent files are managed by macOS for the
Open Recentworkflow. - Exports are written only to locations you explicitly choose.
Feedback and support
For feedback, bug reports, or feature requests, email support@losko.de.
© 2026 Sascha Losko — Obscure Essentials. All rights reserved.